There are an incredible number of government information resources concerning Native Americans available online. The Native American Documents Project at California State University, San Marcos makes a number of historically significant government publications available. In addition, the Avalon Project at the Yale Law School put online all government statutes and treaties concerning Native American Tribes . A project at Oklahoma State University makes the same information available in a different interface. The 1941 GPO publication Handbook of Federal Indian Law is available online here.
The National Museum of the American Indian always has online exhibitions very much worth visiting. In addition, the Smithsonian Institution has a wonderful site, American Indian History and Culture, which documents Native American collections in the Institution's collections.
In terms of current policy, the EPA maintains the American Indian Environmental Office, which handles environmental issues on Indian lands. The U.S. Census Bureau has a webpage devoted to statistical information on American Indian and Alaska Native Populations. Other links of interest include the U.S. Senate Committee on Indian Affairs, The Department of Justice's Office of Tribal Justice, and HUD's Office of Native American Programs (ONAP). For the time being, the website of the Bureau of Indian Affairs is offline.